rs2941577

Variant names:

• chr2-54687322-C-T
• rs2941577

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0956 in 152,230 control chromosomes in the GnomAD database, including 745 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.096 (745 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14552 AN: 152112 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0956 AC: 14554 AN: 152230 Hom.: 745 Cov.: 32 AF XY: 0.0941 AC XY: 7001 AN XY: 74438

African (AFR) AF: 0.103 AC: 4286 AN: 41534

American (AMR) AF: 0.0935 AC: 1430 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0427 AC: 206 AN: 4828

European-Finnish (FIN) AF: 0.0781 AC: 828 AN: 10604

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 6993 AN: 68006

Other (OTH) AF: 0.107 AC: 226 AN: 2114

Alfa AF: 0.105 Hom.: 975

Bravo AF: 0.0966

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.44
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2941577; hg19: chr2-54914459;